With Obama as Broker, Israelis and Turkey End Dispute

JERUSALEM — Under persistent prodding from President Obama, Israel and Turkey resolved a bitter three-year dispute on Friday with a diplomatic thaw that will help a fragile region confront Syria’s civil war, while handing the president a solid accomplishment as he closed out his visit to the Middle East.

The breakthrough took place in the most improbable of surroundings: a trailer parked on the tarmac of Ben-Gurion International Airport. Moments before Mr. Obama left for Jordan, Prime Minister Benjamin Netanyahu telephoned the Turkish prime minister, Recep Tayyip Erdogan, and apologized for deadly errors in Israel’s 2010 raid on a Turkish ship that was trying to bring aid to Palestinians in Gaza.

After years of angrily demanding an apology, Mr. Erdogan accepted Mr. Netanyahu’s gesture, and both sides agreed to dispatch envoys to each other’s nations, having recalled them in 2011.

The president’s involvement, a senior American official said, was crucial to both leaders, which is why Mr. Netanyahu scheduled the call before Mr. Obama’s departure from Israel. Mr. Erdogan insisted on speaking to Mr. Obama first before the president handed the phone over to Mr. Netanyahu. In the end, the call produced a win-win for all sides.

Mr. Obama achieved reconciliation between two of the United States’ most important allies, while Turkey and Israel won good will with the White House, important for two nations that have made ties to the United States central to their foreign policies. Turkey and Israel, along with Jordan, have also been three pillars of stability for the United States as it confronts a civil war in Syria that threatens to spill beyond its borders and destabilize the broader region.

“Both of us agreed the moment was ripe,” Mr. Obama said of Mr. Netanyahu at a news conference later in Amman, Jordan. He cautioned that the détente was a “work in progress” and that Turkey and Israel would continue to have significant disagreements as they mended fences. American officials say both countries are still “working the issue” of dropping criminal charges against four current and former top Israeli military officials that Turkey had indicted in the flotilla raid, and of determining Israel’s compensation to Turkey.

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President Obama; Prime Minister Benjamin Netanyahu, second from left; and President Shimon Peres at the Holocaust museum.CreditDoug Mills/The New York Times

Mr. Obama reiterated his support for Jordan, too, announcing after a meeting with King Abdullah II that the United States would provide an additional $200 million in aid to help Jordan with the burden of caring for 460,000 Syrian refugees who have flooded into the country.

Israel and Turkey have a host of shared economic and security interests, and both are concerned about the unraveling situation in Syria. Turkey also could play a strategic role in Washington and Jerusalem’s efforts to stop Iran from developing a nuclear weapon, as well as in resolving the Israeli-Palestinian conflict.

It was the Palestinian issue that opened the rift between the two, when Israeli commandos raided the Turkish ship, the Mavi Marmara, as it was trying to break Israel’s blockade of Gaza to deliver supplies. Nine people were killed in clashes on board, prompting an international outcry, several investigations and a rebuke by the United Nations.

“The prime minister made it clear that the tragic results regarding the Mavi Marmara were unintentional and that Israel expresses regret over injuries and loss of life,” a statement issued by Mr. Netanyahu’s office said.

Mr. Erdogan’s office, in turn, said he had accepted the apology “on behalf of the Turkish people,” and that in his conversation with Mr. Netanyahu he had emphasized their nations’ shared history and prior eras of friendship and cooperation.

The call’s timing came as a surprise after a visit by Mr. Obama that was intensely symbolic and, publicly at least, tightly focused on Iran, Syria and the peace process. Mr. Obama used his trip to convince the Israeli public that he was a strong supporter and ally — credibility he then hoped to use to persuade the Israelis that it was safe, and wise, to earnestly embrace negotiations with Palestinians. Public reaction suggested that Mr. Obama did win the public trust, but it was not at all clear that he would achieve the second goal and prompt any significant movement in the long-stalled peace process.

Though important, the Turkey-Israel feud was less complex than those other problems. Defusing it may be the only immediate, concrete achievement Mr. Obama can claim from his visit here, beyond a broad sense that he has improved his standing with the Israeli public.

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President Obama met Friday with King Abdullah II, right, at his palace in Amman and pledged an additional $200 million to help Jordan care for Syrian refugees.CreditLarry Downing/Reuters

Still, the Obama administration has been working intensively for months, even years, to repair the breach, according to Israeli, American and Turkish officials. Mr. Obama said he had raised it regularly with both leaders, as did former Secretary of State Hillary Rodham Clinton. But Mr. Netanyahu had resolutely refused to issue an apology, despite having coming close to agreeing before the recent election in Israel.

Changes in Mr. Obama’s cabinet and in the makeup of Israel’s new government helped ease the situation, officials said.

The new secretary of state, John Kerry, made it a focus of his visit to Ankara, the Turkish capital, this month, officials said. American diplomats prodded Mr. Erdogan to step back from his recent comments comparing Zionism to fascism, which in turn made it easier for them to get Mr. Netanyahu to make a move. The worsening situation in Syria, officials said, was also a catalyst.

“Obama and Kerry worked on it the last two months, and they made the difference,” said Alon Liel, a former Israeli ambassador to Turkey. “With the whole region in such turmoil, it was very difficult that the two allies of the United States in the region were not cooperating. There was no dialogue whatsoever on the high political level and even on the high diplomatic level.”

Ersin Kalaycioglu, a foreign policy professor at Istanbul’s Sabanci University, saw the ice-breaking as an American move to strengthen Israel’s position among hostile neighbors.

“America does not want to leave any conflicts behind as it confines its power projection in the region,” he said. “Israel’s good relations with Turkey would put more pressure on Iran.”

In addition to the apology, the two leaders also discussed further easing the restrictions on imports to Gaza, which had been the goal of the Mavi Marmara, one of a series of flotillas Israel that has blocked from approaching the Palestinian coastal enclave.

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President Obama with King Abdullah II of Jordan.CreditDoug Mills/The New York Times

There was no specific new arrangement made, but Israeli officials said they would consider allowing more goods in as long as rockets were not fired from Gaza into their country, as they were Thursday morning.

“The two leaders remained in consensus to work together for the improvement of the humanitarian situation on the Palestinian soil,” said the statement from Mr. Erdogan’s office.

Izzet Sahin, a leader of the I.H.H., an Istanbul-based charity that led the Mavi Marmara flotilla, said the apology, compensation and discussion of import restrictions amounted to “an important statement,” but added, “We have to see the implementation before we honor our dead.”

Avigdor Lieberman, the former foreign minister who many saw as an obstacle to an Israeli apology, on Friday called it a “grave mistake” that would undermine his nation’s military.

While a renewed alliance with Turkey could eventually lead to progress on other fronts, Mr. Obama left Israel on a wave of good will but lacking public, tangible take-homes on Syria, Iran and the Palestinians.

Mark Regev, Mr. Netanyahu’s spokesman, reiterated Friday that the prime minister was ready to resume negotiations if President Mahmoud Abbas of the Palestinian Authority would do so without preconditions. But he said that Mr. Obama’s visit had not shifted Israel’s position.

“We want to see a peace process where both sides are playing a part to move the process forward — we want to see a process that is a two-way street,” Mr. Regev said. “It can’t just be that one side makes demands and the other side makes concessions.”

Mr. Obama also made three symbolic pilgrimages on Friday: meeting with Christian leaders at the Church of the Nativity in Bethlehem; laying wreaths and stones at the graves of Theodor Herzl, the founder of modern Zionism, and Yitzhak Rabin, the slain prime minister and peacemaker; and visiting Yad Vashem, Israel’s Holocaust museum.

A version of this article appears in print on , on Page A1 of the New York edition with the headline: With Obama as Broker, Israelis and Turkey End Dispute Over Ship Raid. Order Reprints | Today’s Paper | Subscribe